Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-12 13:20:21 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for HiTC on nebbiolo1


To the developers/maintainers of the HiTC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiTC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 904/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.40.0  (landing page)
Nicolas Servant
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/HiTC
git_branch: RELEASE_3_15
git_last_commit: 35a87db
git_last_commit_date: 2022-04-26 11:10:49 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HiTC
Version: 1.40.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings HiTC_1.40.0.tar.gz
StartedAt: 2022-08-11 20:30:40 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 20:34:24 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 224.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HiTC.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings HiTC_1.40.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/HiTC.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiTC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
directionalityIndex: no visible global function definition for
  ‘subjectHits’
directionalityIndex: no visible global function definition for
  ‘queryHits’
getBlocsIndex: no visible global function definition for ‘Rle’
getExpectedCountsMean: no visible global function definition for ‘Rle’
normLGF: no visible global function definition for ‘glm.nb’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts : <anonymous>: no visible global function
  definition for ‘seqlevels<-’
divide,HTCexp-HTCexp: no visible global function definition for
  ‘queryHits’
divide,HTCexp-HTCexp: no visible global function definition for
  ‘subjectHits’
isBinned,HTCexp: no visible global function definition for
  ‘countMatches’
substract,HTCexp-HTCexp: no visible global function definition for
  ‘queryHits’
substract,HTCexp-HTCexp: no visible global function definition for
  ‘subjectHits’
Undefined global functions or variables:
  Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
directionalityIndex 18.140  0.604  18.748
CQC                  6.368  0.128   6.497
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/HiTC.Rcheck/00check.log’
for details.



Installation output

HiTC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL HiTC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘HiTC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HiTC)

Tests output


Example timings

HiTC.Rcheck/HiTC-Ex.timings

nameusersystemelapsed
CQC6.3680.1286.497
HTCexp-class2.1690.1362.306
HTClist-class1.1460.0161.164
Nora_5C0.2130.0000.213
binningC1.2090.0041.214
directionalityIndex18.140 0.60418.748
discretize000
export.my5C000
exportC000
extractRegion0.3240.0000.325
getAnnotatedRestrictionSites000
getExpectedCounts1.0160.3251.220
getPearsonMap0.5030.0240.527
getRestrictionFragmentsPerChromosome0.0000.0000.001
import.my5C0.0800.0160.097
importC0.0000.0000.001
intervalsDist0.3810.0480.429
mapC4.4240.1484.573
normICE000
normLGF000
pca.hic0.4690.0040.473
removeIntervals0.250.000.25
setGenomicFeatures000
setIntervalScale0.8300.0040.834